rewrote metastats command in c++, added mothurRemove function to handle ~ error....

[mothur.git] / distancecommand.cpp

diff --git a/distancecommand.cpp b/distancecommand.cpp
index 4bdeaaeb5d9b388ac56fc2553f57dc10c0d598d9..b69b93d85c44c1fa89d08d49c0fb478b2f0cb242 100644 (file)
--- a/distancecommand.cpp
+++ b/distancecommand.cpp
@@ -255,7 +255,7 @@ int DistanceCommand::execute(){
                                
                if (output == "lt") { //does the user want lower triangle phylip formatted file 
                        outputFile = outputDir + m->getRootName(m->getSimpleName(fastafile)) + "phylip.dist";
-                       remove(outputFile.c_str()); outputTypes["phylip"].push_back(outputFile);
+                       m->mothurRemove(outputFile); outputTypes["phylip"].push_back(outputFile);
                        
                        //output numSeqs to phylip formatted dist file
                }else if (output == "column") { //user wants column format
@@ -268,10 +268,10 @@ int DistanceCommand::execute(){
                                rename(column.c_str(), tempcolumn.c_str());
                        }
                        
-                       remove(outputFile.c_str());
+                       m->mothurRemove(outputFile);
                }else { //assume square
                        outputFile = outputDir + m->getRootName(m->getSimpleName(fastafile)) + "square.dist";
-                       remove(outputFile.c_str());
+                       m->mothurRemove(outputFile);
                        outputTypes["phylip"].push_back(outputFile);
                }
                
@@ -449,7 +449,7 @@ int DistanceCommand::execute(){
        #endif
        
 #endif
-               if (m->control_pressed) { outputTypes.clear();  delete distCalculator; remove(outputFile.c_str()); return 0; }
+               if (m->control_pressed) { outputTypes.clear();  delete distCalculator; m->mothurRemove(outputFile); return 0; }
                
                #ifdef USE_MPI
                        MPI_Comm_rank(MPI_COMM_WORLD, &pid); 
@@ -472,17 +472,17 @@ int DistanceCommand::execute(){
                        if (outputFile == column) { 
                                string tempcolumn = column + ".old";
                                m->appendFiles(tempcolumn, outputFile);
-                               remove(tempcolumn.c_str());
+                               m->mothurRemove(tempcolumn);
                        }else{
                                m->appendFiles(outputFile, column);
-                               remove(outputFile.c_str());
+                               m->mothurRemove(outputFile);
                                outputFile = column;
                        }
                        
                        if (outputDir != "") { 
                                string newOutputName = outputDir + m->getSimpleName(outputFile);
                                rename(outputFile.c_str(), newOutputName.c_str());
-                               remove(outputFile.c_str());
+                               m->mothurRemove(outputFile);
                                outputFile = newOutputName;
                        }
                }
@@ -492,7 +492,7 @@ int DistanceCommand::execute(){
                        }
                #endif
                
-               if (m->control_pressed) { outputTypes.clear();  delete distCalculator; remove(outputFile.c_str()); return 0; }
+               if (m->control_pressed) { outputTypes.clear();  delete distCalculator; m->mothurRemove(outputFile); return 0; }
                
                delete distCalculator;
                
@@ -571,7 +571,7 @@ void DistanceCommand::createProcesses(string filename) {
                //append and remove temp files
                for (int i=0;i<processIDS.size();i++) { 
                        m->appendFiles((filename + toString(processIDS[i]) + ".temp"), filename);
-                       remove((filename + toString(processIDS[i]) + ".temp").c_str());
+                       m->mothurRemove((filename + toString(processIDS[i]) + ".temp"));
                }
 #endif
        }
@@ -935,7 +935,7 @@ int DistanceCommand::convertMatrix(string outputFile) {
                //m->openInputFile(outfile, in);
                
                while(!in.eof()) {
-                       if (m->control_pressed) { in.close(); remove(outfile.c_str()); out.close(); return 0; }
+                       if (m->control_pressed) { in.close(); m->mothurRemove(outfile); out.close(); return 0; }
                        
                        in >> first >> second >> dist; m->gobble(in);
                                
@@ -970,7 +970,7 @@ int DistanceCommand::convertMatrix(string outputFile) {
                in.close();
                out.close();
                
-               remove(outfile.c_str());
+               m->mothurRemove(outfile);
                
                return 1;
                
@@ -1025,7 +1025,7 @@ int DistanceCommand::convertToLowerTriangle(string outputFile) {
                //m->openInputFile(outfile, in);
                
                while(!in.eof()) {
-                       if (m->control_pressed) { in.close(); remove(outfile.c_str()); out.close(); return 0; }
+                       if (m->control_pressed) { in.close(); m->mothurRemove(outfile); out.close(); return 0; }
                        
                        in >> first >> second >> dist; m->gobble(in);
                                
@@ -1064,7 +1064,7 @@ int DistanceCommand::convertToLowerTriangle(string outputFile) {
                in.close();
                out.close();
                
-               remove(outfile.c_str());
+               m->mothurRemove(outfile);
                
                return 1;
                
@@ -1135,7 +1135,7 @@ bool DistanceCommand::sanityCheck() {
                string name1, name2;
                float dist;
                while (!inDist.eof()) {
-                       if (m->control_pressed) {  inDist.close(); outDist.close(); remove(outputFile.c_str()); return good;  }
+                       if (m->control_pressed) {  inDist.close(); outDist.close(); m->mothurRemove(outputFile); return good;  }
                
                        inDist >> name1 >> name2 >> dist; m->gobble(inDist);
                        
@@ -1152,10 +1152,10 @@ bool DistanceCommand::sanityCheck() {
                outDist.close();
                
                if (good) {
-                       remove(column.c_str());
+                       m->mothurRemove(column);
                        rename(outputFile.c_str(), column.c_str());
                }else{
-                       remove(outputFile.c_str()); //temp file is bad because file mismatch above
+                       m->mothurRemove(outputFile); //temp file is bad because file mismatch above
                }
                
                return good;